Another common factor is that everyone I hear talking at the gym appears to have had “viral pneumonia” within the last week or so… have they…really? Or is this the “new trendy diagnosis” a ploy by GPs to stop antibiotic prescribing or an exaggeration for just feeling rough! Do viruses even cause pneumonia?
 
Do viruses really cause pneumonia?
Well, the simple answer to this is yes, viruses do indeed cause pneumonia. There are approximately 20 cases of pneumonia per 1,000 population per year but of which only 6-7 per 1,000 population per year are viral. However, some pneumonias are in fact a mixture of bacterial and viral infection; 1-3 of these viral pneumonias have a bacterial co-pathogen e.g. Streptococcus pneumoniae, Haemophilus influenzae, Mycoplasma pneumoniae. It’s commonly believed that the virus causes damage to the lung allowing the bacterium to take advantage but could it be vice versa… the research is ongoing to look at this!
 
So the annual incidence of viral pneumonia is 6-7 per 1,000 population per year. Compare this to the fact that every adult gets 2-3 viral upper respiratory tract infections per year (3,000 per 1,000 population per year) and you realise that what most people are calling their new trendy “viral pneumonia” is actually a bad upper respiratory tract infection… but “I’ve got an upper respiratory tract infection” does #tag so well. Viral pneumonia does happen; it’s just not that common!
 
The most common causes of viral pneumonia are:

• Influenza Virus (7.1%) – the most severe form of viral pneumonia causing seasonal epidemics with a high mortality
• Rhinovirus (12.7%) – the most commonly isolated virus but usually a co-pathogen rather than the only infecting microorganism
• Parainfluenza Virus (3.4%) – causes severe infections in immunosuppressed patients, especially those with haematological malignancies or post bone marrow transplantation
• Coronavirus (2.8%) – usually a co-pathogen but severe infections can occur including Severe Acute respiratory Syndrome (SARS) and Middle-Eastern Respiratory Syndrome (MERS)
• Adenovirus (2.2%) – causes severe infections in immunosuppressed patients, especially those with haematological malignancies or post bone marrow transplantation
• Respiratory Syncytial Virus (RSV) (1.2%) – common seasonal epidemics which can be severe; especially bad in infants in whom it causes bronchiolitis
• Human Metapneumovirus (hMPV) (0.9%) - usually a co-pathogen rather than the only infecting microorganism

 
How do viruses cause pneumonia?
Until the advent of molecular detection of microorganisms it was thought that the lung was sterile. However, we now know that the lung has its own normal flora (microbiome) consisting of anaerobic bacteria such as Prevotella spp. and Veilonella spp. as well as microaerophilic Streptococcus spp. (microaerophilic bacteria prefer a slightly lower oxygen level than aerobic bacteria, which is all rather weird being that the lungs are full of O2!). This normal flora is kept in check, and at low numbers, by the normal host lung immunological defence mechanisms.
 
Pneumonia occurs when:

1. A microorganism of particularly high virulence enters the lung (usually by microaspiration) e.g. Influenza Virus, RSV
2. There is a large inoculum of microorganism; viruses are not part of the normal lung flora and so large inoculums of any of these microorganisms can cause pneumonia
3. There is a defect in the normal host defence of the lung which allows other viruses or bacteria to cause infection e.g. smoking damaging alveolar white blood cells, Rhinovirus, hMPV or Coronavirus

 
How do you diagnose viral pneumonia?
Firstly you need to diagnose pneumonia. Pneumonia is diagnosed based on a combination of symptoms and signs as well as imaging.
 
The symptoms and signs of pneumonia are:

• Cough PLUS one other lower respiratory tract symptom (shortness of breath, purulent sputum, chest pain)
• New focal chest signs on examination (reduced chest movement, dull percussion, bronchial breathing, increased tactile vocal fremitus and vocal resonance)
• One systemic symptom (fever, sweats, shivers, aches and pains)

• No other explanation

 
In primary care, pneumonia is diagnosed based on these symptoms and signs above; in hospital the diagnosis needs to be confirmed by the presence of new infiltrates on a chest x-ray. However it is impossible to tell the difference between viral and bacterial pneumonia on a chest x-ray as the x-ray is just showing inflammation, not the microorganism.
 
Once the diagnosis of pneumonia is made you need to find a virus in order to say it is viral pneumonia.
 
There are two main ways of “finding” viruses:

• Enzyme-linked Immunoassays (EIA) – serum tests looking for the immune response (usually IgM antibodies) against the specific viruses
• Polymerase Chain reaction (PCR) – on sputum looking for the genetic material of the viruses themselves

 
PCR is the best way of detecting viruses as IgM is notorious for giving false positive results. PCR is very specific (it proves the presence of the virus) but can be a little insensitive (it can give a negative result even though the virus is there); specificity of >98% and sensitivity of >90%. The main drawbacks to PCR are that it is relatively expensive (>£100 per test for a multi-target PCR), it requires a good sputum sample from the lung not the upper respiratory tract and it will detect all viruses or co-pathogens even if they are only in the upper respiratory tract (15% of people can have viruses in their upper respiratory tracts at any one time).
 
How is viral pneumonia treated?
The only commonly used antivirals for pneumonia are targeted against Influenza Virus (Oseltamivir and Zanamivir). For all of the other viruses treatment is usually supportive with respiratory support, adequate hydration and antipyretics. Immunocompromised patients are occasionally treated with antivirals but these are usually last ditch efforts as toxicity can be more of a problem and the benefits are small e.g. RSV can be treated with Ribavirin (teratogenic) and Adenovirus can be treated with Cidofovir (bone marrow toxicity).
 
As there is no specific treatment for most viral pneumonias it might seem wasteful to do a £100 PCR to find a virus, however the value would lie in being able to stop antibacterials that might have side effects as well as potentially being able to discharge patients earlier and save hospital bed days.
 
Is bacterial pneumonia worse than viral pneumonia?
Pneumonia is pneumonia is pneumonia… (however “Old-monia” is apparently worse for those around the infected person!) There doesn’t appear to be much difference in outcome from either bacterial pneumonia or viral pneumonia; the mortality is the same and is related to the infections’ severity not cause.
 
So have the people I heard talking about their “viral pneumonia” really had pneumonia? Probably not, it’s not that common and it is more likely that they have had an upper respiratory tract infection. I’m not trying to belittle people’s illnesses but in my experience people do have a habit of exaggerating how unwell they were, maybe to justify time off work or away from the gym, it’s just human nature. We should remember getting over a bout of illness takes time; allow yourself the time without feeling guilty. I signed off for a week a few weeks ago as I had “Old-monia”, my wife wouldn’t take my temperature so I couldn’t have a fever and therefore I couldn’t really be ill! I think those that are really unwell tend to play down their illnesses, either to try and appear healthier than they actually are or perhaps it’s just that “stiff upper lip” of the British… either way that’s just as much human nature as exaggeration.
 
Perhaps the real answer is to get a better pair of headphones and try not to hear what others are saying in the gym… or better yet skip the gym and stay at home in the warmth… now there’s an idea, let’s look up what box set I “need” to watch… Text arrives… “are we going to the gym tonight!?” Rats!!!

Well that’s what the Telegraph newspaper says so it must be true!
 
Okay, let’s try and bring this down a peg and look at what is really the story behind the sensationalist headline. Whilst it is sometimes amusing to read these stories, the lack of balance with resulting scare-mongering is frustrating.
 
A study has been performed by Public Health England in association with the National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, looking at the presence of Flaviviruses in deer and deer ticks in the UK. Gosh! What a mouthful, even abbreviated that’s NIHRHPRUEZI, yeah! So we’ll just call them “Liverpool” from now on!!!
 
Anyhow back to the Flaviviruses! Some Flaviviruses cause tick-borne encephalitis (TBE), a condition transmitted by ticks of the Ixodes spp. which usually feed on deer. There are three main types of TBE based upon geographical area:

• European (Scandinavia down to the Adriatic)
• Far-Eastern (Russia, China, Japan)
• Siberian (Siberia and the Baltic)

The Microbiologist picked up the phone to call out a result.
 
“This one looks interesting” he said to himself even though he knew he had been told never to use the word interesting in relation to microbiology…. Ever…!
 
“You have a baby boy on the ward with salmonellosis, what’s the story?” he asked when the Paediatric SHO answered the phone.
 
“He’s a six week old who developed bloody diarrhoea a couple of days ago and started vomiting. He was febrile and looked septic so we started him on empirical IV Ceftriaxone.”
 
“Any pets?” asked the Microbiologist.
 
“He’s only 6 weeks old, why would he have any pets?” answered the tired junior.
 
“Not him, the family; specifically reptiles. Any snakes or lizards?”
 
“I have no idea.”
 
“Well carry on with the IV Ceftriaxone as he has a Salmonella species in his blood culture and call me back about the reptiles… no wait, I’ll come up and ask myself.”
 
The junior doctor hung up. Muttering to himself about mad Microbiologists he wandered off to get on with some other work.
 
So why did the Microbiologist want to know about reptiles? Was he just mad or was there method to his madness?

“I think my patient has TB but they have had BCG in the past so I was wondering what might mimic TB?” asked the junior doctor.
 
“They could have TB” replied the Microbiologist.
 
“But they’ve had their BCG” replied the junior doctor, gosh he’s not listening, he’s probably playing spider solitaire, thought the junior doctor, as he could hear clicking in the background.
 
“Yes, but they could still have TB” repeated the Microbiologist.
 
Deep inhale… “Yes, but they have a BCG scar on their arm, they have been immunised in the past, so they can’t have TB” stated the junior doctor firmly.
 
You’d think the junior’s right, wouldn’t you? But I’m blogging on it so, who is right? Can you get TB having been immunised with BCG? Let’s talk about BCG first…

Warning: this blog mite make you itch!
 
The Oncology Registrar sat in the Multidisciplinary Team meeting looking thoroughly miserable. They looked like they hadn’t slept for ages, and whilst this can often be the case for junior doctors, the Microbiologist knew the registrar had only just returned from annual leave.
 
Whilst trying to pay attention to the patient discussions the Microbiologist watched as the poor Registrar kept scratching at his hands and arms.
 
As the meeting drew to a close, the Microbiologist wandered over…they can’t help but meddle!!!
 
“You look like your suffering” he said sympathetically, when in fact he was “itching” to make a shrewd diagnosis!!!
 
“Yeah. My hands and arms are really itchy, and it was worse in that room as it was so hot. I think I’m allergic to something”.
 
The Microbiologist wasn’t so sure.
 
“Show me your hands” he said.
 
The Registrar helpfully held out his hands which looked red and inflamed.
 
Looking closely whilst not touching (oooh, all those germs!!! He’d seen the Infection Control hand plates in the past!!!) the Microbiologist soon realised the likely cause of the problem.

At the weekly Neonatal Unit Multidisciplinary Team Meeting the Microbiologist was asked about a baby with Cytomegalovirus infection. The baby had been born at term but was very small, below the 3rd centile. Other than the size of the baby there were no other concerns during the pregnancy. The baby had looked otherwise well and was behaving normally. A number of tests had been done to look for a reason why the baby might be small and a urine sample had tested positive for Cytomegalovirus DNA by PCR.
 
The Neonatologists wanted to know what they should do next and the MDT members looked at the Microbiologist expectantly, who started to feel somewhat uncomfortable under all those stares…

The Biomedical Scientist walked hesitantly into the duty Microbiologists office.
 
“We have a mould growing in a blood culture” they said.
 
“You mean a yeast?” asked the Microbiologist.
 
“Nope, definitely a mould” replied the BMS.
 
“A contaminant maybe?” asked the Microbiologist again, now starting to hope this was the case.
 
“Nope, definitely not a contaminant” replied the BMS.
 
“Please tell me this was handled in Cat 3?” asked the Microbiologist again, starting to sound worried and thinking he should maybe put the Health and Safety Executive (HSE) telephone number into his phone!
 
“Nope, not in Cat 3” replied the BMS looking crest fallen, “but it should have been… I think it’s Talaromyces marneffei”
 
The Microbiologist just stared at them lost for words… why did it always happen when he was on duty?!
 
What is Talaromyces marneffei?
T. marneffei is a dimorphic fungus; it has two types of growth depending on the temperature (a bit like cheese! Cheese is a solid block when in the fridge but when sliced and put on toast under a grill it’s all gooey!!!) It used to be called Penicillium marneffei, but like many other microorganisms it has undergone a recent name change just to keep us on our toes.

On his way to review a ward patient the Microbiologist was stopped by one of the Consultant Physicians and asked about a different patient. These “corridor consultations” are fairly frequent in medicine and often lead to significant decisions about patient care, it’s important to document them though; remember, “if it isn’t written down then you didn’t do it”.
 
“I have a patient who I have been seeing in clinic who I think might have tuberculosis, but the sputum and bronchoalveolar lavage cultures are negative. Is there anything else that can present in the same way that I might be missing?” the Physician asked.
 
“Why do you think they have TB?” asked the Microbiologist, thinking is this related to those pesky Tabby Cats!?

The Microbiologist was slowly meandering through the daily authorisation, trying to stay awake and not authorise something important without seeing it first… honestly we do really pay attention but it can be a little dull authorising out more than a hundred urine results a day!
 
Suddenly something caught their eye. A wound swab was growing Candida auris. The Microbiologist sat up straight in his chair (I am notorious for slouching at the duty desk!) and picked up the phone to find out more.